Access the portal at: shepherdpay.com
What You Need to Know
Most payment processing happens in Shepherd, not the portal.
The portal is for account management and exceptional situations — not routine transactions.
Your Gateway Portal login is separate from your Shepherd login.
They are two different systems with different credentials. If you cannot log in to the portal, contact merchant@shepherd.vet — Shepherd Support cannot access or reset portal credentials.
If you process a payment in the portal, you must also record it in Shepherd manually. Payments processed in the portal do not sync to Shepherd automatically. Skipping this step will cause your financial records and invoices to be out of sync.
Each staff member who needs portal access must have their own user account.
Do not share login credentials between staff members.
Portal users are automatically deactivated after 90 days of inactivity.
A warning is sent around day 85. If a user is deactivated, contact merchant@shepherd.vet for reactivation.
Batch close time is set in the portal.
Transactions that settle before the batch closes are processed that day. Adjust this setting to align with your clinic's end-of-day workflow.
Initial Setup
When you first receive access to the Gateway Portal, complete the following steps before using it.
Set Your Password
Open the welcome email from Shepherd Pay
Click the link to set your password
Choose a secure password and confirm it
Log in to the portal
Configure Email Notifications
Email notifications alert you when batches close or when account activity occurs.
Log in to the portal
Navigate to Settings > Notifications
Enter the email address(es) that should receive batch and account notifications
Save
Managing Users
Each staff member who needs access to the Gateway Portal requires their own user account. User accounts control who can log in, view transactions, and process payments in the portal.
Add a New User
Log in to the portal
Navigate to Settings > Users
Click Add User
Enter the staff member's name, email address, and assign a role
Save — the staff member will receive an email to set their password
Deactivate a User
When a staff member leaves your clinic, deactivate their portal account promptly.
Navigate to Settings > Users
Locate the user
Select Deactivate
Deactivating a portal user does not automatically remove their Shepherd
login. Both systems must be updated independently.
PCI Compliance and User Management
Maintaining accurate user records in the portal is part of your clinic's PCI compliance obligations. Accounts belonging to staff who no longer work at your clinic should be deactivated promptly to prevent unauthorized access. Portal users are also automatically deactivated after 90 days of inactivity — if an active staff member's account is deactivated for this reason, contact merchant@shepherd.vet for reactivation.
Batch Settings
A batch is the group of transactions that settle together at a set time each day. All approved transactions in the current open batch are submitted for settlement when the batch closes. Batching is automatic — you do not need to manually close a batch each day.
Funding timing: If a batch closes before 7:45 PM EST, funds are typically deposited the next business day. If a batch closes after 7:45 PM EST, funding may be delayed by one additional business day.
Change Your Batch Close Time
Log in to the portal
Navigate to Settings > Batch
Update the batch close time to your preferred time
Save
Changing the batch close time affects when transactions settle and when funds are deposited. Coordinate with your practice manager before making changes. EMV terminal batch timing may be separate from portal batch timing — contact merchant@shepherd.vet if you are unsure whether a setting applies to your terminals.
Export Batch Data
Batch data can be exported for reconciliation or accounting purposes.
Navigate to Reporting > Batch History
Select the date range or specific batch you want to export
Click Export and select your preferred file format
Save the file
Looking Up a Transaction
Use the Gateway Portal to search for and confirm transaction details that are not visible in Shepherd — such as whether a payment successfully processed, is pending, has settled, was batched, or was voided or refunded.
Log in to the portal
Navigate to Reporting > Transaction Search
Search by date, amount, card details, transaction status, or batch information
If a payment appears in Shepherd but not in the portal:
The payment was likely recorded in Shepherd with the Shepherd Pay toggle off, meaning no card transaction was sent through Shepherd Pay. Review the payment history in Shepherd to confirm how it was recorded. Payments taken without Shepherd Pay will not appear in the portal and will not be included in Shepherd Pay deposits.
Processing a Manual Payment in the Portal
Use this workflow only when Shepherd is unavailable and a payment must be processed immediately — for example, during a system outage or connectivity issue.
This is a fallback workflow only. If Shepherd is available, always take payments through Shepherd instead.
Step 1: Process the Payment in the Portal
Log in to the Shepherd Pay Gateway Portal
Navigate to Virtual Terminal
Enter the payment amount
Enter the card details (number, expiration, CVV, billing zip)
Click Charge
Note the transaction ID and authorization code from the confirmation screen — you will need these for Step 2
Step 2: Record the Payment in Shepherd
After the portal payment is approved, record it in Shepherd to keep your financial records accurate.
Open the client's invoice in Shepherd
Click Take Payment
Toggle Shepherd Pay off — this prevents Shepherd from charging the card again
Select Credit Card as the payment method
Enter the payment amount
Add a note with the transaction ID or authorization code from the portal
Click Check Out
This step is required. If it is skipped, the invoice will remain unpaid in Shepherd and the payment will not appear in Shepherd's reporting.
Video Walkthrough
Frequently Asked Questions
My portal login says deactivated — what do I do?
Portal users are automatically deactivated after 90 days of inactivity, with a warning email sent around day 85. Shepherd Support cannot reactivate portal users. Contact merchant@shepherd.vet to have your account reactivated.
I forgot my portal password — how do I reset it?
On the portal login page, click Forgot Password and enter your email address. You will receive a reset link. If you do not receive the email, check your spam folder or contact merchant@shepherd.vet.
My deposit amount does not match what I see in Shepherd — why?
Deposit totals may not match Shepherd reports exactly due to timing and transaction differences, including batch close time, pending vs. settled transactions, refunds or voids, surcharges, payments recorded in Shepherd with Shepherd Pay toggled off, or transactions processed in the portal but not recorded in Shepherd. Use the Gateway Portal to review batched and settled transactions, then compare against payments recorded in Shepherd for the same date range. For account-specific deposit questions, contact merchant@shepherd.vet.
A transaction shows as approved in the portal but is not in Shepherd — what happened?
The payment was likely processed in the portal during a Shepherd outage and not recorded in Shepherd afterward. Record the payment manually in Shepherd following Step 2 above, and make sure the Shepherd Pay toggle is off so the card is not charged again.
Do I need to manually close my batch every day?
No. Shepherd Pay batching is automatic. Transactions are batched at the end of the day based on your configured batch close time.
Who do I contact for Gateway Portal help?
For portal access, credentials, batching, funding, merchant account, or transaction processing questions, contact merchant@shepherd.vet. For questions about how a payment appears on an invoice or client account inside Shepherd, contact Shepherd Support via the in-app chat.